Naming issues

[bcdaniels]

We need to update network_modifier.py to put Cell Collective (and maybe other) network files into a format that BoolODE will recognize. In particular, BoolODE does not like underscores in gene names.

[bcdaniels]

Also note that running BoolODE in parallel currently hides error messages, making it harder to debug these issues.

[bcdaniels]

Pull request #5 attempts to address this issue